During the first five years of the PHENIX project we have developed a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that we have built and made available to the community. The algorithms are tightly linked and made easily accessible to the user through the PHENIX Wizards and the PHENIX GUI. These crystallographic libraries, algorithms, and automation form a framework that we will use during the next five years to develop a system that can begin with reduced X-ray diffraction data from any experimental source (anomalous diffraction, isomorphous replacement, molecular replacement), automatically solve and complete the structure, generate a model or set of models most consistent with the data, and prepare the models and data for deposition. Ultimately we plan to produce minimally biased atomic coordinates with little or no human intervention. The impact of our system will extend beyond the realm of structural genomics, allowing all crystallographers to solve challenging biological problems.